TB-Profiler result

Run: SRR6964556
Summary

Run ID: SRR6964556

Sample name:

Date: 2024-04-16T11:21:11.373646

Number of reads: 2321756

Percentage reads mapped: 99.47

Median coverage: 51.0

Strain: lineage1.1.2;lineage3

Spoligotype:

Drug-resistance: RR-TB

Download CSV Download TXT Download JSON
Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage3 East-African-Indian RD750 0.44
lineage1.1.2 Indo-Oceanic RD239 0.53
lineage1.1 Indo-Oceanic RD239 0.55
lineage1 Indo-Oceanic RD239 0.58
Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations WHO confidence Comment
rifampicin rpoB p.Ser450Leu Assoc w R
isoniazid
ethambutol embB p.Tyr319Cys Assoc w R
pyrazinamide pncA c.-12T>C Assoc w R
streptomycin rrs n.906A>G Uncertain significance Mutation from literature
gid c.253delG Assoc w R
fluoroquinolones
moxifloxacin
ofloxacin
levofloxacin
ciprofloxacin
aminoglycosides
amikacin
capreomycin
kanamycin
cycloserine
ethionamide
clofazimine
para-aminosalicylic_acid
delamanid
bedaquiline
linezolid
Drug resistance-Associated Mutations: This table reports mutations found in candidate resistance genes which have been associated with drug resistance
Gene Chromosome position Mutation Type Estimated fraction Drugs Confidence Comment
rpoB 761155 p.Ser450Leu missense_variant 0.38 rifampicin Assoc w R
rrs 1472751 n.906A>G non_coding_transcript_exon_variant 0.5 streptomycin Uncertain significance Mutation from literature
pncA 2289253 c.-12T>C upstream_gene_variant 0.48 pyrazinamide Assoc w R
embB 4247469 p.Tyr319Cys missense_variant 0.49 ethambutol Assoc w R
gid 4407949 c.253delG frameshift_variant 0.32 streptomycin Assoc w R
Non-Associated Mutations: This table reports mutations found in candidate resistance genes which have not been associated with drug resistance
Gene Chromosome position Mutation Type Estimated fraction Drugs Confidence
gyrB 6112 p.Met291Ile missense_variant 0.55 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrB 6124 c.885C>T synonymous_variant 0.56 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 7362 p.Glu21Gln missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 7585 p.Ser95Thr missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 7655 c.354G>C synonymous_variant 0.63 levofloxacin
moxifloxacin
gyrA 8452 p.Ala384Val missense_variant 0.58 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 9143 c.1842T>C synonymous_variant 0.48 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 9304 p.Gly668Asp missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
Rv0010c 13298 p.Ile87Met missense_variant 0.68 isoniazid Not assoc w R
Rv0010c 13304 c.255G>A synonymous_variant 0.63 isoniazid Not assoc w R - Interim
Rv0010c 13460 c.99T>C synonymous_variant 0.63 isoniazid Not assoc w R
fgd1 491742 c.960T>C synonymous_variant 1.0 clofazimine Not assoc w R
pretomanid
delamanid Not assoc w R - Interim
mshA 574748 c.-600G>A upstream_gene_variant 0.6 ethionamide
isoniazid Uncertain significance
Rv0565c 657081 c.390G>A synonymous_variant 0.44 ethionamide Not assoc w R - Interim
Rv0565c 657578 c.-108T>C upstream_gene_variant 0.58 ethionamide
nusG 734116 c.-138T>C upstream_gene_variant 0.5 rifampicin Not assoc w R
rpoB 760490 c.684C>T synonymous_variant 0.39 rifampicin Not assoc w R
rpoB 762434 c.2628T>G synonymous_variant 0.33 rifampicin Not assoc w R
rpoB 763031 c.3225T>C synonymous_variant 1.0 rifampicin Not assoc w R
rpoC 763884 p.Ala172Val missense_variant 0.53 rifampicin Not assoc w R
rpoC 763886 c.517C>A synonymous_variant 0.57 rifampicin Not assoc w R
rpoC 765171 p.Pro601Leu missense_variant 0.61 rifampicin Not assoc w R
rpoC 766466 p.Glu1033Lys missense_variant 0.42 rifampicin Uncertain significance
mmpL5 775639 p.Ile948Val missense_variant 1.0 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
mmpL5 776100 p.Thr794Ile missense_variant 1.0 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
mmpL5 776395 p.Phe696Leu missense_variant 0.52 clofazimine Not assoc w R
bedaquiline Uncertain significance
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
rplC 800357 c.-452C>A upstream_gene_variant 0.59 linezolid Not assoc w R
Rv1129c 1254562 c.-28T>C upstream_gene_variant 1.0 moxifloxacin Not assoc w R
levofloxacin Not assoc w R
rifampicin Not assoc w R
isoniazid Not assoc w R
fbiC 1303051 p.Val41Met missense_variant 0.69 clofazimine Uncertain significance
pretomanid
delamanid Uncertain significance
fbiC 1304232 c.1302G>T synonymous_variant 0.31 clofazimine
pretomanid
delamanid
embR 1417019 p.Cys110Tyr missense_variant 0.5 ethambutol Not assoc w R
embR 1417554 c.-207C>G upstream_gene_variant 0.64 ethambutol
embR 1417793 c.-446C>T upstream_gene_variant 0.5 ethambutol
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 streptomycin
kanamycin
capreomycin
amikacin
rrl 1474722 n.1065T>C non_coding_transcript_exon_variant 0.44 capreomycin Uncertain significance
linezolid
tsnR 1853974 c.369C>T synonymous_variant 0.53 linezolid Not assoc w R
tsnR 1854045 p.Tyr147Cys missense_variant 0.47 linezolid Not assoc w R
tsnR 1854300 p.Leu232Pro missense_variant 1.0 linezolid Not assoc w R
tlyA 1917972 c.33A>G synonymous_variant 1.0 capreomycin Not assoc w R
bacA 2062922 p.Ile603Val missense_variant 0.51 streptomycin Not assoc w R
kanamycin Not assoc w R
capreomycin Not assoc w R
amikacin Not assoc w R
katG 2154724 p.Arg463Leu missense_variant 1.0 isoniazid Not assoc w R
katG 2155217 p.Gly299Ser missense_variant 0.5 isoniazid Uncertain significance
PPE35 2167926 p.Leu896Ser missense_variant 1.0 pyrazinamide Not assoc w R
PPE35 2167983 p.Gly877Asp missense_variant 0.5 pyrazinamide Uncertain significance
Rv1979c 2222308 p.Asp286Gly missense_variant 0.56 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
Rv1979c 2223136 p.Ala10Val missense_variant 0.54 clofazimine Uncertain significance
bedaquiline Uncertain significance
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
Rv1979c 2223314 c.-150C>G upstream_gene_variant 0.56 clofazimine
bedaquiline
pncA 2289047 c.195C>T synonymous_variant 0.48 pyrazinamide Not assoc w R
pncA 2289365 c.-125delC upstream_gene_variant 0.38 pyrazinamide
kasA 2518132 c.18C>T synonymous_variant 0.51 isoniazid
ahpC 2726051 c.-142G>A upstream_gene_variant 0.64 isoniazid
ahpC 2726105 c.-88G>A upstream_gene_variant 0.48 isoniazid Not assoc w R
Rv2477c 2782498 c.1545C>T synonymous_variant 0.48 ethambutol Not assoc w R
moxifloxacin Not assoc w R
streptomycin Not assoc w R - Interim
levofloxacin Not assoc w R
kanamycin Not assoc w R
rifampicin Not assoc w R
amikacin Not assoc w R
Rv2681 2996912 c.174C>T synonymous_variant 0.5 capreomycin Not assoc w R
Rv2752c 3064632 c.1560C>T synonymous_variant 0.62 ethambutol Not assoc w R
moxifloxacin Not assoc w R
levofloxacin Not assoc w R
rifampicin Not assoc w R
isoniazid Not assoc w R
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine
Rv3083 3448443 c.-61A>G upstream_gene_variant 0.43 ethionamide
Rv3083 3448714 p.Asp71His missense_variant 0.76 ethionamide Uncertain significance
lpqB 3624486 p.Asp142Gly missense_variant 0.56 bedaquiline Uncertain significance
rifampicin Not assoc w R
mtrB 3625065 p.Met517Leu missense_variant 1.0 bedaquiline Uncertain significance
rifampicin Not assoc w R
mtrB 3626467 c.147G>A synonymous_variant 0.47 bedaquiline Not assoc w R - Interim
rifampicin Not assoc w R
alr 3841473 c.-53G>A upstream_gene_variant 0.46 cycloserine
clpC1 4040517 p.Val63Ala missense_variant 0.61 pyrazinamide Not assoc w R - Interim
panD 4044740 c.-459C>T upstream_gene_variant 0.62 pyrazinamide
panD 4044872 c.-591C>T upstream_gene_variant 0.43 pyrazinamide
glpK 4138377 p.Val460Ala missense_variant 0.65 ethambutol Not assoc w R
moxifloxacin Not assoc w R
streptomycin Not assoc w R
levofloxacin Not assoc w R
rifampicin Not assoc w R
isoniazid Not assoc w R
glpK 4139183 c.572delG frameshift_variant 0.65 ethambutol Uncertain significance
moxifloxacin Uncertain significance
streptomycin Uncertain significance
levofloxacin Uncertain significance
rifampicin Uncertain significance
isoniazid Uncertain significance
embC 4239593 c.-270G>A upstream_gene_variant 0.56 ethambutol Not assoc w R
embC 4240671 p.Thr270Ile missense_variant 0.69 ethambutol Not assoc w R
embC 4241042 p.Asn394Asp missense_variant 0.7 ethambutol Not assoc w R
embC 4242075 p.Arg738Gln missense_variant 0.54 ethambutol Not assoc w R
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embA 4243217 c.-16C>A upstream_gene_variant 0.34 ethambutol Uncertain significance
embA 4243848 p.Val206Met missense_variant 0.65 ethambutol Not assoc w R
embA 4244167 p.Ala312Val missense_variant 0.67 ethambutol Uncertain significance
embA 4245969 p.Pro913Ser missense_variant 0.53 ethambutol Not assoc w R
embB 4247646 p.Glu378Ala missense_variant 0.64 ethambutol Not assoc w R
embB 4247684 p.Leu391Val missense_variant 0.71 ethambutol
ubiA 4269387 p.Glu149Asp missense_variant 0.63 ethambutol Not assoc w R
ubiA 4269606 c.228T>C synonymous_variant 0.58 ethambutol Not assoc w R
ethA 4326432 p.Leu348Phe missense_variant 0.64 ethionamide Uncertain significance
whiB6 4338595 c.-75delG upstream_gene_variant 1.0 capreomycin Not assoc w R
amikacin Not assoc w R
kanamycin Not assoc w R
whiB6 4338603 c.-82C>T upstream_gene_variant 0.51 capreomycin Not assoc w R
amikacin Not assoc w R
kanamycin Not assoc w R
whiB6 4338732 c.-211C>T upstream_gene_variant 1.0 capreomycin
amikacin
kanamycin
gid 4407588 c.615A>G synonymous_variant 1.0 streptomycin Not assoc w R
gid 4407873 c.330G>T synonymous_variant 0.72 streptomycin Not assoc w R